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[Refactor] Update file organisation rules for GitHub-native vs portable assets #291

@ashleyshaw

Description

@ashleyshaw

Is your code refactoring request related to a problem?

The current file-organisation guidance says operational assets should stay under .github, which conflicts with the new portable plugin structure.

Parent epic: #282.

Describe the Refactoring / Review Task

Update .github/instructions/file-organisation.instructions.md and related references so they distinguish GitHub-native repo files from portable AI plugin assets.

Use Case

Maintainers and AI agents need unambiguous placement rules during and after the restructure.

Acceptance Criteria

  • Guidance defines GitHub-native files.
  • Guidance defines portable plugin assets.
  • Guidance maps reports and active project files.
  • Existing links to file organisation guidance still resolve.
  • No production assets are moved.
  • Documentation updated as needed.
  • PR uses correct branch prefix refactor/.

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